Contacts of the helix formed by residues 315 - 327 (chain F) in PDB entry 4XLN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 315 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307F ALA* 3.3 9.8 - - - +
313F GLY 3.6 8.0 + - - +
314F TRP* 1.3 74.0 - - - +
316F ALA* 1.3 64.0 - - - +
317F LYS* 3.4 9.5 + - - +
318F ARG* 2.8 38.9 + - - +
319F VAL* 3.2 21.3 + - - +
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Residues in contact with ALA 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808C ARG* 5.6 7.9 - - - +
303F TYR* 3.4 36.8 + - + +
304F GLU* 4.4 5.7 - - + +
315F ASP* 1.3 75.4 - - - +
317F LYS* 1.3 58.6 + - - +
319F VAL* 3.1 3.5 - - - +
320F GLU* 2.9 32.1 + - - +
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Residues in contact with LYS 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714C ASP* 4.3 21.6 + - - -
808C ARG* 5.1 10.2 - - - +
820C ARG* 5.7 3.2 - - - +
315F ASP* 3.3 10.1 + - - +
316F ALA* 1.3 79.4 - - - +
318F ARG* 1.3 58.6 + - - +
320F GLU* 3.7 22.0 + - - +
321F GLU* 2.9 36.3 + - - +
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Residues in contact with ARG 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282F THR* 4.6 11.7 - - - +
312F PRO 4.8 1.0 + - - -
313F GLY* 4.0 18.9 + - - -
314F TRP* 3.3 61.8 - - + +
315F ASP* 2.8 24.3 + - - +
316F ALA 3.3 0.2 - - - -
317F LYS* 1.3 75.4 - - - +
319F VAL* 1.3 60.6 + - - +
321F GLU* 3.0 8.5 + - + +
322F THR* 2.9 38.4 + - + +
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Residues in contact with VAL 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F LEU* 3.7 26.2 - - + +
303F TYR* 3.6 31.6 - - + +
306F ILE* 3.7 22.4 - - + -
307F ALA* 4.0 3.4 - - + -
314F TRP* 4.0 15.0 - - + -
315F ASP 3.2 13.1 + - - +
316F ALA* 3.1 16.6 - - - +
318F ARG* 1.3 78.5 - - - +
320F GLU* 1.3 55.7 + - - +
322F THR* 3.1 7.7 + - - -
323F LEU* 2.9 37.2 + - + +
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Residues in contact with GLU 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714C ASP* 5.6 0.7 - - - -
808C ARG* 3.0 40.1 + - - -
817C PRO* 3.6 13.2 - - + +
818C GLY* 3.0 32.2 + - - +
819C VAL 4.1 0.9 + - - -
303F TYR* 3.9 21.1 - - + -
316F ALA 2.9 19.7 + - - +
317F LYS* 3.7 32.2 + - - +
319F VAL* 1.3 78.2 - - - +
321F GLU* 1.3 55.9 + - - +
323F LEU* 3.4 3.1 + - - +
324F LYS* 2.9 27.4 + - - +
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Residues in contact with GLU 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818C GLY* 6.4 0.4 - - - -
35D ARG* 5.6 5.2 + - - +
317F LYS* 2.9 26.1 + - + +
318F ARG* 3.0 13.2 + - + +
320F GLU* 1.3 74.4 - - - +
322F THR* 1.3 62.5 + - + +
324F LYS* 2.8 38.6 + - - +
325F ILE* 3.0 32.5 + - + +
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Residues in contact with THR 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F MET* 4.4 23.1 - - - -
282F THR* 4.9 5.6 - - - +
283F ILE* 4.5 10.1 - - - +
286F LEU* 3.1 25.4 - - + +
314F TRP* 4.2 8.6 - - + -
318F ARG* 2.9 26.4 + - + +
319F VAL* 3.1 13.9 + - - -
321F GLU* 1.3 78.7 - - + +
323F LEU* 1.3 56.5 + - - +
325F ILE* 3.3 13.1 + - + +
326F ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C PRO* 4.1 18.6 - - + +
286F LEU* 5.8 2.7 - - + -
303F TYR* 3.6 30.3 - - + +
319F VAL* 2.9 25.3 + - + +
320F GLU* 3.4 6.5 - - - +
322F THR* 1.3 76.0 + - - +
324F LYS* 1.3 64.3 + - - +
326F ALA* 3.2 21.9 + - + +
327F GLN* 3.8 7.2 + - - +
21P A 5.7 9.6 - - + +
22P T 6.0 2.5 - - + -
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Residues in contact with LYS 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713C ARG* 3.2 29.3 - - - +
714C ASP 3.4 14.1 + - - +
715C THR 5.0 0.2 - - - -
716C LYS* 3.6 25.3 - - - +
817C PRO* 4.5 20.9 - - + +
818C GLY* 4.5 14.6 - - - -
533D GLY* 4.5 11.7 - - - -
320F GLU 2.9 12.7 + - - +
321F GLU* 2.8 26.4 + - - +
323F LEU* 1.3 76.4 - - - +
325F ILE* 1.3 61.7 + - + +
327F GLN* 3.2 33.9 + - - +
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Residues in contact with ILE 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.4 44.2 - - + +
35D ARG* 3.9 26.2 - - - +
271F ARG* 5.1 0.3 - - - -
273F ILE* 4.6 9.4 - - + +
275F ILE* 5.1 8.0 - - + +
279F MET* 3.9 24.2 - - + -
283F ILE* 5.4 0.2 - - - -
321F GLU* 3.0 31.6 + - + +
322F THR* 3.8 10.3 - - + +
323F LEU 3.3 0.2 - - - -
324F LYS* 1.3 77.1 - - + +
326F ALA* 1.3 65.3 + - - +
327F GLN 3.3 8.7 + - - +
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Residues in contact with ALA 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271F ARG* 3.6 13.8 - - - +
283F ILE* 4.3 17.0 - - + -
322F THR 2.9 14.0 + - - +
323F LEU* 3.2 21.5 - - + +
324F LYS 3.2 0.8 - - - -
325F ILE* 1.3 78.6 - - - +
327F GLN* 1.3 61.9 + - - +
328F GLU* 3.7 0.7 + - - +
22P T 2.7 46.4 - - + +
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Residues in contact with GLN 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816C LYS* 5.9 2.4 - - - +
817C PRO* 5.9 2.4 - - - +
532D GLY 5.7 0.4 + - - -
533D GLY 3.8 21.6 + - - -
534D ARG* 4.5 25.2 + - - +
271F ARG* 4.9 0.3 - - - -
273F ILE* 4.3 9.9 - - - +
323F LEU* 3.8 6.0 + - - +
324F LYS* 3.2 29.0 + - - +
325F ILE 3.4 8.5 - - - +
326F ALA* 1.3 81.6 - - - +
328F GLU* 1.3 70.1 + - - +
329F PRO* 4.4 0.3 - - - +
20P A 5.4 7.9 - - + -
21P A 6.5 1.3 - - + -
22P T 4.7 1.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il